ALBERT — All Library Books, journals and Electronic Records Telegrafenberg

1

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Reply to Haeseker: Snake River salmon survival [Biological Sciences] (2013)

Rechisky, E. L., Welch, D. W., Porter, A. D.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-09-11

Description: In our report (1), we set out to explicitly control for the ecological differences Haeseker (2) cites so that we could assess the effect of a critical policy issue: whether Snake River dam passage results in poorer early marine survival of juvenile Snake River spring Chinook salmon. Thus, we selected...

Keywords: Letters

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Reply to Crispin et al.: sFc model [Biological Sciences] (2013)

Sondermann, P., Pincetic, A., Maamary, J., Lammens, K., Ravetch, J. V.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-09-18

Description: We recently published a model (1) that proposes a molecular basis for the anti-inflammatory properties of sialylated IgG Fc (sFc), resulting from its observed shift in receptor specificity from FcγRs to dendritic cell-specific intercellular adhesion molecule-3-grabbing nonintegrin (DC-SIGN)/CD23, a consequence of changes to the structure of the CH2 domain that...

Keywords: Letters

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Not all nanoparticles are high-density lipoprotein [Biological Sciences] (2013)

Cormode, D. P., Fisher, E. A., Stroes, E. S. G., Mulder, W. J. M., Fayad, Z. A.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-09-18

Description: High-density lipoprotein (HDL) is a natural nanoparticle that transports cholesterol from peripheral tissues to the liver and also transports other lipids, proteins, enzymes, and microRNAs. HDL–cholesterol levels are negatively correlated with the risk of cardiovascular events. HDL has also been shown to reduce inflammation and to improve endothelial function (1)....

Keywords: Letters

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Crystal structure of sialylated IgG Fc [Biological Sciences] (2013)

Crispin, M., Yu, X., Bowden, T. A.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-09-18

Description: Intravenous Ig consists of pooled human serum IgG and is widely used as an anti-inflammatory agent. The fraction of IgG that is α2,6-sialylated exhibits anti-inflammatory activity and sialylation is proposed to enable binding to the cell surface lectin, dendritic cell-specific intercellular adhesion molecule-3-grabbing nonintegrin (DC-SIGN) (1). In a recent article...

Keywords: Letters

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Calcium amendment and forest hydraulic efficiency [Biological Sciences] (2013)

Smith, K. T., Shortle, W. C.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-10-02

Description: Green et al. (1) report 2 y of increased evapotranspiration (ET; calculated as the difference between total precipitation and total runoff) and decreased water yield following watershed-scale amendment of soil with wollastonite (CaSiO3) at the Hubbard Brook Experimental Forest in the White Mountains of New Hampshire. The watershed manipulation study...

Keywords: Letters

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Allen, T. A., Fortin, N. J.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-10-02

Description: To shed light on the evolution of episodic memory, we recently integrated the behavioral evidence across species with a comparative analysis of the underlying neurobiology and neural mechanisms (1). We conclude that fundamental features of episodic memory are present in mammals and birds and that a similar neural circuit could...

Keywords: Letters

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Estimation in collective decisions [Biological Sciences] (2013)

Perez–Escudero, A., Miller, N., Hartnett, A. T., Garnier, S., Couzin, I. D., de Polavie&jnodot;a, G. G.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-09-11

Description: Miller et al. (1) demonstrate, by confronting groups of fish with three options, that information can be effectively integrated, allowing consensus despite no individual being aware of the consensus option. The different ways in which the conflict can be resolved allow testing of collective decision-making theories. The experimental results show...

Keywords: Letters

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Synthetic HDL mimic [Biological Sciences] (2013)

Marrache, S., Dhar, S.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-09-18

Description: We thank Cormode et al. (1) for their interest and comments on our recent article in PNAS (2). We would like to emphasize that throughout our article, we call our nanoparticle as “synthetic high-density lipoprotein (HDL) mimic” not “HDL-like.” The very definition of the term “synthetic mimic” implies that the...

Keywords: Letters

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Monarchs are almost certainly not true navigators [Biological Sciences] (2013)

Mouritsen, H., Derbyshire, R., Stalleicken, J., Mouritsen, O. O., Frost, B. J., Norris, D. R.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-09-25

Description: Oberhauser et al. (1) raise several concerns related to our recent PNAS paper (2), all of which we address here. To test for true navigation, one can use translocation experiments (3) and modeling (4). Truly navigating animals know where they are relative to their goal and thus can correct their...

Keywords: Letters

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Monarch navigation mechanisms still unknown [Biological Sciences] (2013)

Oberhauser, K. S., Taylor, O. R., Reppert, S. M., Dingle, H., Nail, K. R., Pyle, R. M., Stenoien, C.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-09-25

Description: Mouritsen et al. (1) used a flight-simulator experiment and recapture data to examine two hypotheses: whether monarchs use true navigation or a vector-navigation strategy. In the flight-simulator experiment, flight directions of wild-captured, migratory butterflies were assessed near their capture location, and then ∼2,500 km west. The authors’ finding that monarchs...

Keywords: Letters

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11

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Human frontal lobe scaling [Biological Sciences] (2013)

Smaers, J. B.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-09-25

Description: All studies from the last 15 y of collecting data on primate frontal lobe volumes share one central result: allometric scaling of the human frontal lobe is not larger than expected. Recent studies collecting data on the prefrontal cortex confirm this result, but additionally indicate human prefrontal white matter specialization....

Keywords: Letters

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Human frontal lobe size [Biological Sciences] (2013)

Barton, R. A., Venditti, C.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-09-25

Description: Contrary to Smaers’s claim (1) that all recent studies find “allometric scaling of the human frontal lobe is not larger than expected,” one study (2) clearly claimed otherwise. Smaers’s own studies (3) are somewhat more ambiguous on this point, and he contradicts himself here by stating that “the conclusion that...

Keywords: Letters

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Episodic-like memory brain systems [Biological Sciences] (2013)

Rattenborg, N. C., Martinez-Gonzalez, D.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-10-02

Description: In their review in PNAS, Allen and Fortin use a comparative neuroanatomical approach to gain insight into the evolution of episodic memory (1). The authors suggest that, as in humans, episodic-like memory in nonhuman mammals depends on a system consisting of the hippocampus, parahippocampal region, and prefrontal cortex (PFC), and,...

Keywords: Letters

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Lacking evidence of hydraulic efficiency changes [Biological Sciences] (2013)

Green, M. B., Bailey, A. S., Bailey, S. W., Battles, J. J., Campbell, J. L., Driscoll, C. T., Fahey, T. J., Lepine, L. C., Likens, G. E., Ollinger, S. V., Schaberg, P. G.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-10-02

Description: After calcium silicate amendment to an entire watershed at the Hubbard Brook Experimental Forest, evapotranspiration (ET) increased by ∼20% for 2 y, broadly attributed to a fertilization of tree physiology (1). We suggested that the increase in ET most likely arose from enhanced transpiration due to increased stomatal conductance (gs)...

Keywords: Letters

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Richness increases with habitat diversity [Biological Sciences] (2013)

Hortal, J., Carrascal, L. M., Triantis, K. A., Thebault, E., Meiri, S., Sfenthourakis, S.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-06-12

Description: In the paper by Allouche et al. (1), the authors suggested that species richness decreases at high levels of habitat diversity because the area available per habitat decreases [area–heterogeneity tradeoff hypothesis (AHTO)]. They showed a hump-shaped relationship between Catalonian bird richness and altitudinal range in grid cells, the authors’ surrogate...

Keywords: Letters

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Biomineralization toolkit proteome [Biological Sciences] (2013)

Ramos-Silva, P., Marin, F., Kaandorp, J., Marie, B.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-06-12

Description: In an interesting work published recently in PNAS, Drake et al. (1) presented a proteomic study of the skeleton from the stony coral Stylophora pistillata. This study identified proteins that are associated to the mineral phase (i.e., that potentially contribute to shape the skeleton). In other words, this set of...

Keywords: Letters

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Coral skeletal proteome response [Biological Sciences] (2013)

Drake, J. L., Mass, T., Haramaty, L., Zelzion, E., Bhattacharya, D., Falkowski, P. G.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-06-12

Description: We thank Ramos-Silva et al. (1) for their thoughtful comments on our work recently published in PNAS (2). We agree that careful cleaning of biomineral samples is indeed necessary for appropriate proteomic analysis. However, we respectfully disagree with their interpretation of our cleaning methods and our decision to include certain...

Keywords: Letters

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Bird distribution in Spain supports the AHTO [Biological Sciences] (2013)

Allouche, O., Kalyuzhny, M., Moreno-Rueda, G., Pizarro, M., Kadmon, R.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-06-12

Description: Niche theory predicts that species diversity should increase with increased environmental heterogeneity. In contrast to this prediction, breeding bird diversity in Catalonia shows an overall unimodal heterogeneity–diversity relationship (HDR). We attributed this result to a fundamental geometric constraint termed the area–heterogeneity tradeoff (AHTO) (1). Hortal et al. (2) reject our...

Keywords: Letters

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Slow proton exchange and multiple folding species [Biological Sciences] (2013)

Campos, L. A., Munoz, V.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-04-03

Description: In contrast to the implications of the letter by Huang et al. (1), our previous work unambiguously showed that the protein BBL under denaturing conditions is a single, partly unfolded state (one-state folding) rather than a mix of folded and unfolded molecules (two-state folding) (2). This conclusion was based on...

Keywords: Letters

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Epigenomic socioeconomic studies [Biological Sciences] (2013)

Suderman, M., Borghol, N., Pappas, J. J., McArdle, W., Racine, A., Hallett, M. T., Pembrey, M. E., Hertzman, C., Power, C., Szyf, M.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-04-03

Description: In a recent issue of PNAS, Lam et al. (1) identified three CpG sites associated with early-life socioeconomic status (SES) in adult blood DNA. The authors observed that this small number of associated CpG sites “appears to be at odds” with the 1,252 gene promoters found in our study of...

Keywords: Letters

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Confounding factors in DNA methylation analysis [Biological Sciences] (2013)

Lam, L. L., Emberly, E., Fraser, H. B., Neumann, S. M., Chen, E., Miller, G. E., Kobor, M. S.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-04-03

Description: In our paper (1), we primarily questioned whether the statistical approach used by Borghol et al. (2) was justified, because treating neighboring probes as independent can lead to inflated P value significance. We are glad to see that in their Letter, Borghol et al. do not dispute this (3). We...

Keywords: Letters

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Nonrepresentative study fish confound inferences [Biological Sciences] (2013)

Haeseker, S.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-09-11

Description: Close examination of the methods, assumptions, and results of Rechisky et al. (1) indicate that their results are confounded by nonrepresentative tagging, rearing, and release factors, and that critical assumptions are inconsistent with available data. Thus, the authors’ conclusions regarding hydrosystem-related delayed mortality are overreaching and unsupportable. Nonrepresentative fish with...

Keywords: Letters

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Reply to Steinman and Wang: Involvement of the p150 isoform of the RNA editing enzyme ADAR1 in embryonic lethality [Letters (Online Only)] (2011)

Ward, S. V., George, C. X., Samuel, C. E., Oldstone, M. B. A.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-06-15

Description: In their letter, Steinman and Wang (1) raise the possibility that p110 expression may be affected by specific gene targeting of the p150 isoform of adenosine deaminase 1 (ADAR1), similar to the concerns raised in the letter by Matthaei et al. (2). Although Steinman and Wang acknowledge that the levels of the constitutive exon 1B-containing transcript encoding the p110 isoform of ADAR1 were similar in both p150+/− and p150−/− MEF cells derived from gene-targeted embryos compared with MEF cells derived from WT embryos as shown in our article (3), they suggest that protein expression may have been affected as a...

Keywords: Letters

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Algal ice-binding proteins change the structure of sea ice [Letters (Online Only)] (2011)

Raymond, J. A.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-06-15

Description: Krembs et al. (1) reported that extracellular polymeric substances (EPS) produced by a sea ice diatom, Melosira, created convoluted ice-pore morphologies in sea ice, potentially increasing its habitability and primary productivity. The activity was reduced by heat treatment and glycosidase treatments, suggesting that a glycoprotein was involved. Based on our previous work (2), it is very likely that the active substance is an ice-binding protein (IBP).All sea ice diatoms examined so far secrete similar ∼25 kDa IBPs that bind to ice, distorting its shape as it grows (2). Similar proteins are found in ice-adapted bacteria and fungi (3) and even...

Keywords: Letters

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ADAR1 isoform involvement in embryonic lethality [Letters (Online Only)] (2011)

Steinman, R. A., Wang, Q.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-06-15

Description: Letters to the editor recently published in PNAS (1, 2) challenged and defended a claim made on a recent article (3). Matthaei et al. (1) questioned whether the animal model used by Ward et al. (3) was adequate to support their claim that the P150 isoform of the RNA editing enzyme adenosine deaminase 1 (ADAR1) is required for embryogenesis. We believe the question remains open and present data indicating that a more complete assessment of ADAR1 isoform protein expression in the model of Ward et al. (3) is necessary to draw firm conclusions from it.In mammalian cells, the two major...

Keywords: Letters

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Reply to Mulrooney et al.: Accepting lower precision radiocarbon dates results in longer colonization chronologies for East Polynesia [Letters (Online Only)] (2011)

Wilmshurst, J. M., Hunt, T. L., Lipo, C. P., Anderson, A. J.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-06-08

Description: Mulrooney et al. (1) draw attention to a problem with our table S1 (2), which was unfortunately corrupted in transfer to PNAS (and has since been corrected). The actual database used for our analyses was free of errors (as their reanalysis has shown), thus, our results and conclusions remain unchanged (2).The letter by Mulrooney et al. (1) raises three issues:i) They believe our criteria for classifying dates by accuracy and precision are overly strict (1). However, relaxing standards of acceptance reduces their reliability. Our top down approach (2) may be conservative but results in high-precision, reliable chronologies that can be...

Keywords: Letters

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High-precision dating of colonization and settlement in East Polynesia [Letters (Online Only)] (2011)

Mulrooney, M. A., Bickler, S. H., Allen, M. S., Ladefoged, T. N.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-06-08

Description: Wilmshurst et al. (1) proposed recent and rapid colonization of East Polynesia based on analysis of 1,434 radiocarbon determinations. We commend the development of rigorous and replicable radiocarbon protocols that emphasize accuracy and precision, but we found (i) inaccuracies in their originally published supplementary data table, (ii) problems with their criteria for exclusion and inclusion of valid colonization estimators (i.e., Class 1 dates), and (iii) biases in their statistical analysis.Our review of their originally published 207 Class 1 dates identified 112 incorrectly reported 14C laboratory numbers and 123 misreported conventional radiocarbon ages, with 110 of these reported as at least...

Keywords: Letters

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Replies to Shen, Chen et al., and Yi and Zhou: Linear regression analysis misses effects of winter temperature on Tibetan vegetation [Letters (Online Only)] (2011)

Luedeling, E., Yu, H., Xu, J.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-05-11

Description: We are happy to see that our article (1) has stirred some interest, and we thank the authors of the three letters for their valuable comments (2–4).Shen (2) writes that linear regression could not detect a clear relationship between winter temperatures and beginning of growing season (BGS). This is not surprising. As has been shown many times, the primary driver of spring phenology is spring temperature, and this effect overlays smaller effects of temperature during other parts of the year. To tease such minor effects out of our dataset, we used partial least squares regression, which analyzed the impacts of...

Keywords: Letters

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Delayed spring phenology on the Tibetan Plateau may also be attributable to other factors than winter and spring warming [Letters (Online Only)] (2011)

Chen, H., Zhu, Q., Wu, N., Wang, Y., Peng, C.-H.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-05-11

Description: In their recent paper “Winter and spring warming result in delayed spring phenology on the Tibetan Plateau,” Yu et al. (1) reported an interesting but unexpected result that spring phenology initiated retreating in the mid-1990s, despite continued warming for grasslands (both steppe and meadow) on the Tibetan Plateau, and shortening the length of the growing season of the steppe together with an advancing end. Although we have not observed the same phenomenon in our own many years of field studies on the eastern edge of the Tibetan Plateau, we believed that there were indeed some complicated yet poorly understood dynamics...

Keywords: Letters

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Guanylyl cyclase activity in plants? [Letters (Online Only)] (2011)

Ashton, A. R.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-05-11

Description: Cyclic nucleotides have defined signal transduction roles in animals, fungi, and other diverse eukaryote kingdoms. However, the situation in plants is still not clear after more than 3 decades of investigations reporting evidence for and against a regulatory role for cyclic nucleotides in higher plants. No sequenced higher plant genome contains homologs of the nucleotidyl cyclase genes that are recognizable in diverse eukaryotic kingdoms, including, curiously, the Chlorophyta phylum of the Viridiplantae kingdom. The report of Qi et al. (1) is a recent example of claims that recombinant plant proteins (or their fragments) from diverse protein families have guanylyl cyclase...

Keywords: Letters

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Increasing contamination might have delayed spring phenology on the Tibetan Plateau [Letters (Online Only)] (2011)

Yi, S., Zhou, Z.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-05-11

Description: Using the National Aeronautics and Space Administration (NASA) Global Inventory, Monitoring, and Modeling Studies (GIMMS) Normalized Difference Vegetation Index (NDVI) dataset (1982–2006), Yu et al. (1) found that the trend of advancing spring phenology for alpine steppe and meadow was reversed around 2000, despite the increasing air temperature over the Tibetan Plateau. This phenomenon cannot be explained by changes in precipitation or snow melt. They speculated that the lack of fulfillment of a chilling requirement caused by warming winters could be the reason. This might have significant implications for the ecosystem and economy of the Tibetan Plateau. However, we offer...

Keywords: Letters

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Spring phenology was not consistently related to winter warming on the Tibetan Plateau [Letters (Online Only)] (2011)

Shen, M.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-05-11

Description: Yu et al. (1) reported that the beginning of vegetation growing season (BGS) of the alpine steppe and meadow on the Tibetan Plateau was delayed since the mid-1990s under warming winter and spring (1). They wrote that “this delay appeared to be related to later fulfillment of chilling requirements,” and they suggested that “continued warming may strengthen this effect or even reverse the advancing trend in spring phenology” (1).This idea was proposed earlier for phenology of some species (2) and was tested on the alpine vegetations at the regional level. Using this idea, if winter warming continues and spring warming...

Keywords: Letters

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Information content and word frequency in natural language: Word length matters [Letters (Online Only)] (2011)

Reilly, J., Kean, J.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-05-18

Description: For centuries, scientists have attempted to uncover commonalities that underlie the structure of human languages (1). In a recent issue of PNAS, Piantadosi et al. (2) reported an exciting finding with respect to one unique type of language universal. The authors empirically demonstrated that word length strongly correlated with information content across 11 distinct natural languages. This finding is remarkable in that it directly contravenes Zipf's principle of least effort, which holds that language optimizes communication by spontaneously truncating words as a function of their relative frequency (e.g., television → TV). Simply stated, more frequent words tend to be shorter,...

Keywords: Letters

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Reply to McPherron et al.: Doubting Dikika is about data, not paradigms [Letters (Online Only)] (2011)

Dominguez-Rodrigo, M., Pickering, T. R., Bunn, H. T.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-05-25

Description: We critiqued the claim that bone surface marks on two ∼3.4 Ma fossils from Dikika (Ethiopia) are the earliest evidence of hominin butchery damage (1) by (i) providing a detailed argument showing site- and assemblage-level weaknesses for the claim and (ii) matching those marks morphologically to marks produced on modern bones by trampling in coarse-grained sedimentary substrates, similar to those of the Dikika site (2). The letter by McPherron et al. (3), responding to our critique, completely ignores these substantive issues and, instead, seeks to disqualify our assessment by arguing that we are unwilling to accept a paradigm shift. McPherron...

Keywords: Letters

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Tool-marked bones from before the Oldowan change the paradigm [Letters (Online Only)] (2011)

Mc; Pherron, S. P., Alemseged, Z., Marean, C., Wynn, J. G., Reed, D., Geraads, D., Bobe, R., Bearat, H.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-05-25

Description: Domínguez-Rodrigo et al. (1) critiqued our paper (2), which provided the earliest evidence for stone tool use and animal tissue consumption as evidenced by bones bearing tool-induced marks found at DIK-55 (Dikika, Ethiopia) and dated to 3.39 Ma. Applying a configurational approach, they questioned the bones’ context and without examining or conducting new analysis on the original fossils, argued that all of the Dikika marks resulted from trampling, because a small subset of these marks superficially resembled a small subset of experimentally trampled specimens. Furthermore, they argued (1) that stone tool use and meat consumption before the current consensus dates...

Keywords: Letters

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Reply to Lee: Spatial sorting, assortative mating, and natural selection [Letters (Online Only)] (2011)

Shine, R., Brown, G. P., Phillips, B. L.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-08-03

Description: Lee (1) suggests that spatial sorting will be important only under limited circumstances, that it may often affect traits also subject to natural selection, and that it will enhance the effectiveness of selection by increasing phenotypic variance via positive assortative mating. These points build on the arguments advanced in our original paper, and we broadly agree with him.First, Lee (1) suggests that spatial sorting has only transitory effects. This is certainly true in the case of continuous range expansion (which must stop eventually). However, empirical and theoretical evidence suggests that spatial sorting also may occur continuously at stable range edges...

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Reply to Ferrarini: Strengths and weaknesses of simple competition models [Letters (Online Only)] (2011)

Allesina, S., Levine, J. M.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-08-03

Description: In our work (1), we showed how a largely overlooked mechanism of coexistence based on intransitive competitive relations could be widespread in nature and improve our understanding of biodiversity maintenance. We outlined the basic mechanism, providing a simplified model that can be expanded in several directions. In his comment, Ferrarini (2) raises four points that he believes weaken our approach. Here, we show that these arise from a misunderstanding of our framework, and it is not clear that any of these points would change our fundamental results.First, he stresses how our approach is rooted in zero-sum dynamics and focuses exclusively...

Keywords: Letters

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Reply to Hettinger: Olfaction is a physical and a chemical sense in Drosophila [Letters (Online Only)] (2011)

Franco, M. I., Turin, L., Mershin, A., Skoulakis, E. M. C.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-08-03

Description: We would like to thank Dr. Hettinger (1) for his positive comment on our results showing that flies can discriminate isotopes by smell and are capable of cross-learning between odorants sharing a molecular vibration. Our article (2) demonstrated the presence of a physical (vibrational) component to odor character necessitating a vibration-sensing mechanism, the nature of which was not addressed experimentally and remains to be elucidated. We suggest that it likely involves inelastic electron tunneling, because this is consistent with our experimental data and with Brookes et al. (3), who have shown that an inelastic tunneling mechanism in olfaction is physically...

Keywords: Letters

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Ancient starch: Cooked or just old? [Letters (Online Only)] (2011)

Collins, M. J., Copeland, L.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-06-01

Description: Henry et al. (1) argued for greater sophistication in Neanderthal diets on the basis of the identification of ancient starch granules, some of which—according to changes in morphology—displayed “clear evidence of cooking.” Despite the emphasis on morphology and morphological change, there is no attempt to apply any statistical rigor to their morphology-based identifications (cf. ref. 2); nor is there any attempt to independently confirm that any of the observed structures are indeed composed of starch. Biochemical tests, such as digestion with Bacillus licheniformis 1,4-α-d-glucan-glucanohydrolase (3), can confirm the presence of starch and may give some insight into diagenesis. Similar characterization...

Keywords: Letters

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What about European alvarezsauroids? [Letters (Online Only)] (2011)

Dyke, G. J., Naish, D.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-06-01

Description: Xu et al. (1) reported the alvarezsauroid Linhenykus monodactylus from Inner Mongolia, a confirmed monodactyl Mesozoic dinosaur. Xu et al.’s (1) phylogenetic hypothesis for Linhenykus suggests that it is sister to a clade that includes all other Cretaceous Laurasian alvarezsauroids. On this basis, Xu et al. (1) discussed the paleobiogeographic history of Alvarezsauroidea, concluding that the lineage originated in Asia and then spread via successive dispersal events to South and North America [the earliest known record of this lineage is from the Jurassic of China (2)].Although there is little doubt that Linhenykus is important and interesting from both phylogenetic and...

Keywords: Letters

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Reply to Dyke and Naish: European alvarezsauroids do not change the picture [Letters (Online Only)] (2011)

Xu, X., Sullivan, C., Pittman, M., Choiniere, J. N., Hone, D., Upchurch, P., Tan, Q., Xiao, D., Tan, L., Han, F.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-06-01

Description: Dyke and Naish (1) draw attention to three points that they consider to be “serious shortcomings” of our recent paper on a monodactyl nonavian dinosaur (2). Here, we respond to each point in turn.Our paleobiogeographic hypothesis was based strictly on the phylogenetic tree we recovered (2), which did not include the European alvarezsauroid Heptasteornis because of the extremely fragmentary nature of the known material (3). However, we did include this taxon in a section of our paper (albeit in the SI Appendix) dealing with the biogeography of the Alvarezsauroidea, and even discussed its possible systematic position (2). Because it is...

Keywords: Letters

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Reply to Collins and Copeland: Spontaneous gelatinization not supported by evidence [Letters (Online Only)] (2011)

Henry, A. G., Brooks, A. S., Piperno, D. R.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-06-01

Description: We thank Collins and Copeland (1) for raising the point that a better understanding of starch granule behavior in archaeological settings would be useful. However, we disagree with their assessment that the cooked starch granules we observed on Neanderthal teeth (2) were an effect of diagenesis.To estimate the effect of aging on starch granules, they apply an equation that is used to describe thermal gelatinization of a starch/water system, and we believe their application is not appropriate for predictions about archaeological specimens. Their activation energy estimate derives from experiments in which starches are heated to gelatinization temperatures (≈50–80 °C), far...

Keywords: Letters

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Potential effects of the APOE ϵ2 allele and of family history of Alzheimer's disease on brain amyloid-{beta} in normal elderly [Letters (Online Only)] (2011)

Pomara, N., Bruno, D.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-11-09

Description: Cirrito et al. (1) provided compelling data from investigations in PS1/APP double-transgenic mice that acute and chronic pharmacological manipulations of serotonin signaling were associated with significant reductions in brain interstitial fluid amyloid-β (Aβ) levels and plaque load, respectively. More importantly, they also reported that cognitively intact elderly individuals with a retrospectively obtained history of antidepressant treatment with serotonin reuptake inhibitor (SSRI) drugs, within the past 5 y, showed less brain amyloid load as quantified by PET-Pittsburgh Compound B (PIB) than controls without such a history. In addition, longer duration of SSRI treatment was associated with lower Aβ levels. The authors...

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Reply to Pomara and Bruno: Need for prospective, randomized clinical trial [Letters (Online Only)] (2011)

Sheline, Y. I., Cirrito, J. R.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-11-09

Description: Thank you for giving us an opportunity to reply to the letter to the editor by Pomara and Bruno (1) requesting clarification about the APOE ε2 allele and family history status of the antidepressant-treated group vs. untreated group in our paper in PNAS (2). As pointed out in the letter, there is work describing protective effects of APOE ε2 allele status and higher risk with a family history of Alzheimer's disease. These indeed are potentially important covariates. We did not include APOE ε2 status in the paper because of the small number of individuals in our study sample with this...

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Reply to Karapetyan: Viral synthesis and assembly is unlikely to occur under cell-free PMCA conditions [Letters (Online Only)] (2012)

Chesebro, B., Klingeborn, M., Race, B.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-02-22

Description: The letter to the editor by Karapetyan (1) takes issue with our conclusion in PNAS (2) that the generation of transmissible spongiform encephalopathy (TSE) infectivity in cell-free conditions is against the concept that the TSE infectious agent is a virus. Karapetyan's main point is that poliovirus has been shown to “replicate in a cell-free system” by Wimmer and colleagues (3). We would disagree with the interpretation that these poliovirus experiments are analogous to our protein misfolding cyclic amplification (PMCA) reactions. The divalent cations (Mg2+) and energy sources (ATP and GTP) required for synthesis of viral proteins and nucleic acids, as...

Keywords: Letters

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Earthquake triggering long-term carbon storage [Physical Sciences] (2012)

Zoback, M. D., Gorelick, S. M.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-12-27

Description: Juanes et al. (1) offer three specific arguments in response to our finding that “because even small to moderate-sized earthquakes threaten the seal integrity of CO2 repositories… large-scale [carbon capture and storage (CCS)] is a risky, and likely unsuccessful, strategy for significantly reducing greenhouse gas emissions” (2). We believe all...

Keywords: Letters

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47

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Fluid migration from the Marcellus is possible [Physical Sciences] (2012)

Warner, N. R., Jackson, R. B., Darrah, T. H., Osborn, S. G., Down, A., Zhao, K., White, A., Vengosh, A.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-12-27

Description: Engelder’s letter (1) argues that the sequestration of hydraulic fracturing fluids (HFFs) and brines by imbibition and capillary binding seals the Marcellus Formation and precludes the flow of fluids into overlying formations. This apparently conflicts with our study suggesting that natural connectivity exists between the Marcellus Formation and shallow aquifers...

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No evidence that seismicity causes CO2 leakage [Physical Sciences] (2012)

Juanes, R., Hager, B. H., Herzog, H. J.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-12-27

Description: In a recent Perspective (1), Zoback and Gorelick argued that carbon capture and storage (CCS) is likely not a viable strategy for reducing CO2 emissions to the atmosphere. They argued that maps of earthquake epicenters portray earthquakes occurring almost everywhere, suggesting that Earth’s crust is near a critical state, so...

Keywords: Letters

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Commonalities outweigh differences in emotions [Social Sciences] (2013)

Sauter, D. A., Eisner, F.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-01-16

Description: In a recent study, Jack et al. (1) examined the perception of emotional facial expressions using reverse correlations of viewers’ classifications of randomly generated muscle movements. The authors argued that their findings refute the notion that facial expressions of emotions are shared across human cultures. The reverse-correlation approach is an...

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50

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Facial expressions are different across cultures [Social Sciences] (2013)

Jack, R. E., Garrod, O. G. B., Yu, H., Caldara, R., Schyns, P. G.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-01-16

Description: In response to our work (1), Sauter and Eisner (2) argue, “… [our] strong claims … are not supported by [our] data.” Herein, we show that their arguments are unsubstantiated, primarily reflecting misunderstandings.Sauter and Eisner argue “…[EA] understanding of English emotion terms ... may have been more variable … because...

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COX-2, the dominant source of prostacyclin [Biological Sciences] (2013)

Ricciotti, E., Yu, Y., Grosser, T., Fitz; Gerald, G. A.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-01-16

Description: In a recent issue of PNAS, Kirkby et al. (1) claimed that cyclooxygenase (COX)-1, not COX-2, is the dominant source of prostacyclin (PGI2). This conclusion was based on experiments using a flawed approach to estimating enzyme activity and PGI2 formation and a selective omission of data in the literature.Kirkby et...

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Evidence for vascular COX isoforms [Biological Sciences] (2013)

Mitchell, J. A., Warner, T. D.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-01-16

Description: We welcome interest in our work and encourage debate. As we have published previously (1), we agree with FitzGerald and coworkers (2) that those drugs that inhibit COX-2 have potential deleterious effects upon cardiovascular health, although we disagree with their conclusions that COX-2 drives prostacyclin release in healthy vessels or...

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Worker-biased genes are more diverse and GC-rich [Biological Sciences] (2013)

Kent, C. F., Minaei, S., Harpur, B. A., Zayed, A.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-02-06

Description: We recently showed that genes with worker-biased expression have high guanine–cytosine (GC) content and genetic diversity (1). Hunt et al. (2) conduct additional analyses, which are interesting but do not alter our conclusions (1).Hunt et al. (2) replicate our findings (1) on the association between GC content and worker-biased genes...

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Genome composition, caste, and molecular evolution [Biological Sciences] (2013)

Hunt, B. G., Glastad, K. M., Goodisman, M. A. D.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-02-06

Description: Kent et al. (1) recently investigated genome evolution in the honey bee and proposed “strong links between recombination, biased gene conversion, GC-content evolution, and worker behavior.” However, we feel these connections may be more nuanced than suggested.Kent et al. (1) illustrated dramatically higher guanine and cytosine (GC) content for worker-biased...

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Divergences and mutation rates in humans and apes [Biological Sciences] (2013)

Prufer, K., Langergraber, K. E., Paabo, S., Vigilant, L.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-02-20

Description: In their comment on our recent publication (1), Gibb and Hills (2) raise several issues that we would like to address point by point.First, Gibb and Hills (2) doubt that intergenerational mutation rates can be applied to date events in the past. This argument is mainly based on the idea...

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Mutation rate is not evolution rate [Biological Sciences] (2013)

Gibb, G. C., Hills, S. F. K.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-02-20

Description: Recently in PNAS, Langergraber et al. (1) presented interesting findings regarding body size and generation times in chimpanzees and gorillas. The authors then combined these data with recent whole-genome estimates of human mutation rate per generation to recalibrate previous estimates of divergence times in great apes and humans. The authors’...

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Do not throw equations out [Biological Sciences] (2012)

Gibbons, J.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-11-08

Description: In a recent PNAS paper (1), Fawcett and Higginson analyze citation data for biological journals and conclude that overall citation rate is reduced by including equations in papers. As a serial offender in this regard, I found the paper interesting, if troubling. Here I show that an alternative analysis reveals...

Keywords: Letters

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58

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Mathematical illiteracy impedes biology progress [Biological Sciences] (2012)

Chitnis, N., Smith, T. A.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-11-08

Description: Fawcett and Higginson (1) have shown that citation rates of biology papers with equations in the main text are lower than those of papers without equations. They claim that this implies “heavy use of equations impedes communication among biologists” and recommend that equations be moved to appendixes to improve citation...

Keywords: Letters

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59

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Taxonomic identity of the 30,000-y-old plant [Letters (Online Only)] (2012)

Oxelman, B., Petri, A., Elven, R., Lazkov, G.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-10-10

Description: Yashina et al. (1) reported successful regeneration of whole, fertile plants of Silene stenophylla Ledeb. from immature fruit tissue of Late Pleistocene age using in vitro tissue culture and clonal micropropagation. However, the plants in figures 2–4 in ref. 1 do not possess the diagnostic characters of S. stenophylla. The...

Keywords: Letters

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60

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On the taxonomic status of regenerated plants [Letters (Online Only)] (2012)

Yashina, S., Gubin, S., Maksimovich, S., Yashina, A., Gakhova, E., Gilichinsky, D.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-10-10

Description: We are grateful to Oxelman et al. (1) for their interest in the problem of taxonomic identification of plants regenerated from the fruit tissues of Late Pleistocene age and plants grown from the seeds of extant species growing in the Kolyma Lowland (2). The authors’ arguments regarding the determination of...

Keywords: Letters

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61

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India-Asia collision timing [Letters (Online Only)] (2012)

Aitchison, J. C., Ali, J. R.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-10-03

Description: The contribution of a previously undescribed model by van Hinsbergen et al. (1) to on-going debate on the India-Asia collision is welcomed and will certainly spur further investigation on this important topic. Recognizing the extent of Greater India (GI) is constrained in Gondwana reconstructions by the Wallaby–Zenith plateaus, van Hinsbergen...

Keywords: Letters

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Reply to Aitchison and Ali [Letters (Online Only)] (2012)

van Hinsbergen, D. J. J., Lippert, P. C., Dupont-Nivet, G., McQuarrie, N., Doubrovine, P. V., Spakman, W., Torsvik, T. H.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-10-03

Description: We recently presented a compilation of paleomagnetic data arguing for Cretaceous extension within Greater India. These data imply that a Tibetan Himalayan (TH) microcontinent rifted away from India, opening an oceanic Greater India Basin (GIB) in its wake. Consequently, we postulated a two-stage India-Asia collision at ∼52 and 25–20 Ma...

Keywords: Letters

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63

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Lines of evidence link coral damage to oil spill [Letters (Online Only)] (2012)

White, H. K., Hsing, P.-Y., Cho, W., Shank, T. M., Cordes, E. E., Quattrini, A. M., Nelson, R. K., Camilli, R., Demopoulos, A. W. J., German, C. R., Brooks, J. M., Roberts, H. H., Shedd, W., Reddy, C. M., Fisher, C. R.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-10-03

Description: Our original study (1) used visual inspection as well as biological and geochemical analyses of corals and the surrounding sediment to provide complementary and compelling evidence linking the Deepwater Horizon (DWH) oil spill to the presence of damaged deep-water corals and brittle stars 11 km from the site of the...

Keywords: Letters

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64

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Alternative explanations for coral observations [Letters (Online Only)] (2012)

Boehm, P. D., Carragher, P. D.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-10-03

Description: In the article by White et al. (1) we find that the authors prematurely linked the condition of a single coral community to the Deepwater Horizon oil spill, without evaluating other plausible explanations, including the presence of natural oil and gas seeps near the coral, and the potential for underwater...

Keywords: Letters

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65

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Inconsistent redefining of the carbon spherules [Letters (Online Only)] (2012)

Hardiman, M., Scott, A. C., Collinson, M. E., Anderson, R. S.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-08-22

Description: The recent article by Israde-Alcántara et al. (1) outlined a wide array of purported impact proxies from a lacustrine paleo-record in Lake Cuitzeo, Mexico. These findings were used to support the suggestion of a Younger Dryas (YD) impact event/s. Although most of the purported impact proxies have been described in previous publications (2, 3), this new work extended the range of such markers to Mexico. The article also allowed the proponents of the YD Impact Hypothesis [YDIH] to respond to the many critiques of the YDIH.We wish to discuss Israde-Alcántara et al.’s (1) dismissal of Scott et al.’s (4) recent...

Keywords: Letters

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66

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On the mechanism of CD47 targeting in cancer [Letters (Online Only)] (2012)

Zhao, X. W., Matlung, H. L., Kuijpers, T. W., van den Berg, T. K.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-10-17

Description: The report by Willingham et al. (1) is the most recent in a series of publications from the same group, in which the interaction between the broadly expressed surface molecule CD47 and the myeloid inhibitory receptor SIRPα was implicated as a potential therapeutic target in a variety of malignancies. The...

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67

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Data processing parity [Letters (Online Only)] (2012)

Ma, L., Qiu, Q., Gradwohl, S., Scott, A., Yu, E. Q., Alexander, R., Wiegraebe, W., Yu, C. R.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-10-24

Description: Our recent study (1) has compelled us to reach a conclusion that differs from the widely held idea that chemical features of odors can be systematically mapped to spatial locations in the olfactory bulb (2–4). In an alternative analysis using our data, Yablonka et al. (5) claim to observe substantial...

Keywords: Letters

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Odorant structure to function [Letters (Online Only)] (2012)

Yablonka, A., Sobel, N., Haddad, R.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-10-24

Description: It is widely held that odorant chemical features are mapped onto the olfactory epithelium (1, 2) and bulb (3), such that similar odorants activate common receptors and glomeruli. After applying ultra-high-resolution calcium-indicator dependent imaging to the olfactory bulb, Ma et al. (4) failed to identify a correlation between odorant pairwise...

Keywords: Letters

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Nectar loading in hummingbirds [Letters (Online Only)] (2012)

Kim, W., Gilet, T., Bush, J. W. M.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-04-11

Description: Our article (1) provided a rationale for the vast volume of biological data (20 species of birds, bats, and insects) on optimal nectar concentrations measured in a laboratory setting. The comment of Rico-Guevara and Rubega (2) bears on our footnote, where the relative importance of nectar transport via trapping and capillary rise in the specific case of hummingbird feeding is briefly touched on. The point of their comment is evidently to contest the fact that hummingbirds use capillary suction, so as to defend their claim to the contrary (3).It has been known for over a century that hummingbirds can use...

Keywords: Letters

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Hummingbird feeding mechanics [Letters (Online Only)] (2012)

Rico-Guevara, A., Rubega, M. A.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-04-11

Description: Kim et al. (1), in their recent paper about optimal nectar concentrations based on liquid extraction mechanisms, reported experiments with hummingbirds that we believe are misleading. In a footnote, they cited our recent study (2) on hummingbird feeding mechanics; however, in contrast to our work, they conclude that capillarity is an important mechanism of tongue loading. They support the use of capillarity equations in their model based on a single movie and misguided inferences that we clarify here.In movie S1 of ref. 1, they reported a retraction velocity for a hummingbird tongue of 2 cm/s. We believe this to be...

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71

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Temperature extremes: Changing mean, not variance [Physical Sciences] (2013)

Rhines, A., Huybers, P.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-02-13

Description: Hansen et al. (1) demonstrated that the probability of extremely hot summers has markedly increased because the mean of the distribution of seasonally averaged temperatures has increased. However, the authors also implied that the variance of the distribution has increased, a result that differs from regional studies that show changes...

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72

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Frequency of extreme summer heat [Physical Sciences] (2013)

Hansen, J., Sato, M., Ruedy, R.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2013-02-13

Description: Rhines and Huybers (1) are correct that the decreasing number of measurement stations in recent years contributed slightly to our calculated increase of extreme summer mean temperature anomalies (2). However, the increased frequency of extreme heat anomalies is accounted for mainly by (i) higher mean temperature of recent decades relative...

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Maternal effects can inflate rate of adaptation [Letters (Online Only)] (2012)

Matos, M.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-09-05

Description: An important concern of ex situ conservation programs is how maintenance of populations for several generations in a captive environment affects their performance when these populations are reintroduced to the wild. Although there is some evidence that adaptation to captivity entails a drop in fitness in the wild (1), how...

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74

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Genetic adaptation to captivity [Letters (Online Only)] (2012)

Christie, M. R., Marine, M. L., French, R. A., Blouin, M. S.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-09-05

Description: Matos (1) suggests that maternal effects could also explain the results we presented in a recent paper (2). However, from the outset of our study, we were aware that environmental maternal effects could be a competing explanation for the reduced fitness of hatchery-origin fish. In figure 4 of ref. 2,...

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Lake Cuitzeo Paleoecology inconsistent with ET impact [Letters (Online Only)] (2012)

Gill, J. L., Blois, J. L., Goring, S., Marlon, J. R., Bartlein, P. J., Nicoll, K., Scott, A. C., Whitlock, C.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-08-22

Description: Israde-Alcántara et al. (1) reported evidence for the Younger Dryas (YD) Impact Hypothesis (YDIH), which proposes that an extraterrestrial impact triggered the YD (2). Although most YDIH research has focused on the impact event itself, YDIH proponents, as in this article, have argued that the ecological consequences included “widespread biomass burning, and contributed to the extinction of Late Pleistocene megafauna and to major declines in human populations.” To fully test the YDIH, the authors must evaluate evidence and mechanisms for the ecological consequences of an impact. We believe there are flaws in both the interpretation of the paleoecological evidence reviewed...

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76

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Suspect diamond "impact" proxy [Letters (Online Only)] (2012)

Daulton, T. L.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-08-22

Description: The presence of nanometer-sized diamonds in purported Younger Dryas (YD) boundary-dated sediments, carbon spherules, and Greenland ice was cited as evidence of a YD impact event (1). Although cubic and hexagonal (lonsdaleite) diamond have been found in shocked metamorphosed meteorites and are associated with terrestrial impact structures, cubic diamonds are well known to occur in terrestrial deposits that have no associations with impact processes. For example, submicron and smaller cubic diamond crystals have been found recently in carbonaceous spherules isolated in upper soils from various German and Belgian sites (2). Lacking links to impact structures, these diamonds are evidently not...

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77

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Age models and Younger Dryas Impact [Letters (Online Only)] (2012)

Blaauw, M., Holliday, V. T., Gill, J. L., Nicoll, K.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-08-22

Description: Israde-Alcántara et al. (1) drew on interpretations of a core from Lake Cuitzeo, Mexico to support the Younger Dryas (YD) Impact Hypothesis. A key aspect of their study was identifying and dating the YD interval in the sediments. The authors stated that they recovered impact indicators from a 10-cm-thick zone dating to 12.9 kcal BP but provided no direct numerical age control or chronological uncertainties for this interval. Depending on the carbon sources, 14C ages of bulk lake sediment can be offset by several centuries (2). However, even though the study used bulk 14C dates, no offset was quantified. Dating...

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Inconsistent impact hypotheses for Younger Dryas [Letters (Online Only)] (2012)

Boslough, M.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-08-22

Description: Israde-Alcántara et al. (1) presented evidence from Lake Cuitzeo sediments and argued that it supports the Younger Dryas (YD) impact hypothesis of Firestone et al. (2) for a major extraterrestrial impact event “involving multiple airburst(s) and/or ground impact(s) at 12.9 ka.” Firestone et al. (2) did not specify the details of the impact but proposed that it had “continent-wide effects” and was “most likely a comet.” The YD hypothesis “requires an energy of 107 megatons, equivalent to a 〉4-km-wide comet.” Because no late Pleistocene craters have been identified, Firestone et al. (2) argue for prior fragmentation of a large impactor...

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Reply: Blaauw, Boslough, Daulton, Gill, Hardiman [Letters (Online Only)] (2012)

Israde–Alcantara, I., Bischoff, J. L., De; Carli, P. S., Dominguez–Vazquez, G., Bunch, T. E., Firestone, R. B., Kennett, J. P., West, A.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-08-22

Description: Answer to Blaauw et al. (I.I.-A., J.L.B., R.B.F., J.P.K., A.W.)Blaauw et al. (1) take issue with our age–depth model for the Cuitzeo core. They state that no offset for our accelerator mass spectrometry (AMS) 14C dates was quantified, that our identification of the Cieneguillas tephra is doubtful, that we used an outdated calibration model, and they object to our rejection of six AMS dates in the anomalous zone.Regarding the offset question, dissolved HCO3 in modern Lake Cuitzeo water precipitated in the laboratory as CaCO3 yielded a modern age (US Geological Service laboratory #WW 5645), so the offset is deemed to...

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Response to Kojo [Letters (Online Only)] (2012)

Fox, J. T., Sakamuru, S., Huang, R., Teneva, N., Simmons, S. O., Xia, M., Tice, R. R., Austin, C. P., Myung, K.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-07-25

Description: There are several different mechanisms by which antioxidants induce DNA damage in cultured cells. In a Letter to the Editor, Kojo (1) suggests that one of these mechanisms, the generation of hydrogen peroxide (H2O2) resulting from the exposure of antioxidants to high levels of oxygen in cell culture media, could be primarily responsible for the DNA damage and cell death observed in in vitro studies using resveratrol, genistein, and baicalein (2). Thus, the author questions whether the three antioxidants could act as genotoxins (and by extension, chemotherapeutic agents) in vivo where oxygen concentrations are low. Although this is a valid...

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FOXC1-associated phenotypes in humans [Letters (Online Only)] (2012)

Chakrabarti, S., Ramappa, M., Chaurasia, S., Kaur, I., Mandal, A. K.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-06-13

Description: The transcription factor gene FOXC1 has been implicated with Axenfeld–Rieger syndrome (ARS) in humans. Mutations in this gene have been suggested to contribute to the mechanism leading to developmental defects in the anterior chamber of the eye. In PNAS, Seo et al. (1) demonstrated that mutations in FOXC1 led to corneal angiogenesis in mice and in anterior segment anomalies like ARS in humans. Although the data on mice are very convincing, we provide a different perspective based on our observations in two different patient cohorts with FOXC1 mutations. Our screening of patients (n = 10) with Axenfeld–Rieger anomaly (ARA) for...

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Differentiation of midbrain raphe nuclei [Letters (Online Only)] (2012)

Kranz, G. S., Hahn, A., Savli, M., Lanzenberger, R.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-07-18

Description: The work by Takahashi et al. (1) recently reported a negative association between brainstem serotonin transporters and personality traits such as honesty and rejection to unfairness. They interpret their locus within brainstem to include the dorsal raphe nucleus (DRN) (1). Other than DRN, the median raphe nucleus (MRN) also projects to the forebrain and may be equally important in the serotonergic modulation of cortical activity. Hence, several studies have focused on these two midbrain raphe nuclei with respect to receptor and transporter distributions or anatomical connections. Small nuclei such as DRN and MRN are, however, exceptionally difficult to localize in...

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Antioxidants generate hydrogen peroxide under air [Letters (Online Only)] (2012)

Kojo, S.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-07-25

Description: Antioxidants have received much attention as food factors and drugs. Fox et al. (1) reported that antioxidants induced DNA damage response and cell death in cultured cells. I believe that their study has exceptional importance; however, at the same time, we must be very careful in evaluating antioxidants on the basis of experiments performed under air exposure. The oxygen (O2) concentration in water at 37 °C is ∼200 μM, and O2 also dissolves from the air above the culture medium. Antioxidants easily reduce O2 and generate hydrogen peroxide (H2O2) almost quantitatively, as evidenced by the fact that H2O2 is industrially...

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84

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DC-specific CCR4 expression is required for EAE [Letters (Online Only)] (2012)

Alferink, J., Poppensieker, K., Otte, D.-M., Klotz, L., Scheu, S., Maier, W., Zimmer, A.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-09-12

Description: We appreciate the comments of Othy et al. (1) in response to our recently published article (2). The authors treated myelin oligodendrocyte glycoprotein (MOG)-immunized mice with CC chemokine receptor 4 (CCR4) antagonists and did not observe an altered course of disease (1). Thus, they give a warning on rapid translational...

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Influences of human arrival scenarios [Letters (Online Only)] (2012)

Lima–Ribeiro, M. S., Nogues–Bravo, D., Marske, K. A., Fernandez, F. A. S., Arau&jnodot;o, B., Diniz–Filho, J. A. F.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-09-12

Description: The study by Prescott et al. (1) provides an inspiring quantitative framework for disentangling the effects of humans and climate on megafaunal extinctions, which is essential because their relative importance across time and space remains one of the key missing pieces for solving the late Quaternary extinctions puzzle. However, the...

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CCR4 antagonism in EAE [Letters (Online Only)] (2012)

Othy, S., Topcu, S., Kaveri, S. V., Bayry, J.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-09-12

Description: Experimental autoimmune encephalomyelitis (EAE) is an animal model of multiple sclerosis (MS) wherein T helper (Th) 17 cells are the major pathogenic players orchestrating demyelination of axons. Recently in PNAS, Poppensieker et al. (1) documented a key role on the requirement of CC chemokine receptor 4 (CCR4) in EAE. The...

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Late Quaternary megafaunal extinctions [Letters (Online Only)] (2012)

Prescott, G. W., Williams, D. R., Balmford, A., Green, R. E., Manica, A.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-09-12

Description: In a recent study (1), we analyzed the pattern of late Quaternary megafaunal extinctions in relation to changes in global climate and the timing of human arrival on different landmasses. Lima-Ribeiro et al. (2) write that some of the human arrival scenarios we considered are more plausible than others and...

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AQP4-IgG pathogenicity parallels NMO pathology [Letters (Online Only)] (2012)

Lennon, V. A., Hinson, S. R., Romero, M. F., Fallier-Becker, P., Lucchinetti, C. F.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-06-13

Description: Aquaporin-4 (AQP4) water-channel–specific IgG unifies a spectrum of autoimmune astrocytopathies exemplified by neuromyelitis optica (NMO): relapsing inflammatory myelopathy, optic neuritis, and disorders affecting AQP4-rich circumventricular organs. AQP4-IgG detection in serum distinguishes these disorders from other inflammatory demyelinating disorders. The points of our study (1) were to emphasize that (i) IgG-AQP4 interaction has multiple molecular sequelae that plausibly account for diverse pathology (edema, inflammation, demyelination, and necrosis) and (ii) some outcomes are AQP4 isoform (M1 or M23)-specific. Our study involves immunocytochemistry and freeze-fracture EM of cultured rodent astrocytes, HEK293 cells transfected with non-tagged human AQP4s, Xenopus oocytes expressing GFP-tagged human AQP4s,...

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Reply to Chakrabarti et al. [Letters (Online Only)] (2012)

Seo, S., Singh, H. P., Lacal, P. M., Sasman, A., Fatima, A., Liu, T., Schultz, K. M., Losordo, D. W., Lehmann, O. J., Kume, T.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-06-13

Description: In the 15 years since transcription factor mutation, and subsequently dosage alterations, were shown to account for a proportion of Axenfeld–Rieger syndrome cases, novel phenotypes continue to be defined. As illustrated by the spectrum of FOXC1-attributable CNS anomalies (1, 2), these are frequently present in a subset of cases and only identified by meticulous phenotyping. Our original article in PNAS (3) demonstrated that a proportion of patients with a mutation or altered FOXC1 gene dosage exhibited corneal angiogenesis, confirming our extensive data from multiple murine mutants regarding Foxc1’s role in maintaining corneal avascularity. In keeping with the heterogeneity of transcription...

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Pathogenesis of neuromyelitis optica [Letters (Online Only)] (2012)

Rossi, A., Ratelade, J., Papadopoulos, M. C., Bennett, J. L., Verkman, A. S.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-06-13

Description: Hinson et al. (1) suggested a unique mechanism for the pathogenesis of neuromyelitis optica (NMO), a neuroinflammatory disease caused by binding of an autoantibody (NMO-IgG) to aquaporin-4 (AQP4) on astrocyte plasma membranes. AQP4 is expressed as long (called M1) and short (called M23) isoforms, the latter forming orthogonal arrays of particles (OAPs). Hinson et al. (1) reported that M1-AQP4 is rapidly internalized in cells whereas M23-AQP4 resists internalization, and that NMO-IgG inhibits AQP4 water permeability. They propose that NMO pathogenesis involves NMO-IgG–induced internalization of M1-AQP4 and direct inhibition of AQP4 water permeability, resulting in increased OAP size, enhanced complement-dependent cytotoxicity,...

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Cumulative power calculations are faulty [Letters (Online Only)] (2012)

Piff, P. K., Stancato, D. M., Cote, S., Mendoza–Denton, R., Keltner, D.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-06-20

Description: The conclusions of Francis (1) prompted us to thoroughly review our procedures to check whether bias could in fact have intruded in our recently published studies relating higher social class to increased unethical behavior (2). Selective reporting was definitely not at play: we conducted seven studies and reported our findings for each study. We have also scrutinized our data collection procedures, coding protocols, experimental methods, and debriefing responses. In no case have we found anything untoward. The remaining possibility, then, has been to reexamine the statistical approach that Francis used in inferring bias in our results.We find three significant problems...

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Importance of autumn sea ice to winter snowfall [Letters (Online Only)] (2012)

Li, J., Wu, Z.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-07-11

Description: In their contribution to PNAS, Liu et al. (1) suggested that the recent decline of Arctic sea ice has played a critical role in recent cold and snowy winters in the Northern Hemisphere (NH). This study is very interesting, but we believe it deserves several clarifications.First, in 2010, Wu et al. (2) discovered the importance of autumn Arctic sea ice in triggering regional cold extremes; for example, the 2007–2008 winter, when the NH (particularly East Asia) was struck by severe, record-breaking snowstorms. Liu et al. (1) applied the same idea to East Asia, Europe, and North America. In an interpretation...

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Cements, sulfate, and Burgess Shale preservation [Letters (Online Only)] (2012)

Gaines, R. R., Hammarlund, E. U., Hou, X., Qi, C., Gabbott, S. E., Zhao, Y., Peng, J., Canfield, D. E.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-07-11

Description: In his work, Butterfield (1) makes several claims about carbonate cements in the Walcott Quarry Member of the Burgess Shale, including the contention that they are not regularly associated with fossil-bearing beds. This claim is inaccurate. Each millimeter- to centimeter-scale bed within the interval is cemented by calcite (figures 2–5 in ref. 2), including the exceptionally fossiliferous Great Marella Layer referred to in the work (1), which contains cements dispersed throughout its thickness and a prominently-cemented top (Fig. 1). The work by Butterfield (1) also suggests that the carbonate cements in the Burgess Shale were derived from recrystallization of coarse-grained...

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Burgess Shale-type preservation [Letters (Online Only)] (2012)

Butterfield, N. J.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-07-11

Description: In a recent PNAS paper, Gaines et al. (1) proposed a mechanism of early diagenetic sealing and oxidant limitation to account for the preservation of Burgess Shale-type (BST) fossils (i.e., the “exceptional” preservation of carbonaceous compression fossils in Cambrian-aged marine mudstones) (1). It is an interesting hypothesis, but it raises a number of issues.If early carbonate cementation is the critical factor in BST preservation, then BST biotas should be consistently associated with bed-capping authigenic carbonate. Such a relationship simply does not exist. In terms of anatomical detail, by far the finest BST preservation is found in shales and mudstones with...

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Fungal barcode [Letters (Online Only)] (2012)

Kiss, L.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-07-04

Description: In PNAS, the work by Schoch et al. (1) proposed nuclear ribosomal DNA internal transcribed spacer (ITS) sequences as the sole universal barcode for fungi. The work by Schoch et al. (1) stated that “the proposal will satisfy most fungal biologists but not all” (1).I am among those biologists who are not so satisfied and not really surprised either, because ITS has been the most widely used marker for species identifications in mycology since the development of the first universal primers to amplify this DNA region in fungi. Its use as an unofficial fungal species barcode has also been criticized...

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ITS as fungal DNA barcode [Letters (Online Only)] (2012)

Schoch, C. L., Seifert, K. A.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-07-04

Description: The goals of our study (1) can be summarized as follows in response to the work by Kiss (2):i) To produce enough data across the subphyla defined by the Fungal Tree of Life projects in order to allow a comprehensive statistical comparison of multiple markers as possible barcodes for fungi.ii) To provide convincing arguments for the selection of a different marker than the default DNA barcode CO1 for Fungi.The internal transcribed spacer (ITS) locus was always favored in the mycological community as barcode marker, but no comparative study had yet been attempted using a common set of taxa for multiple...

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Arctic sea ice and winter snowfall [Letters (Online Only)] (2012)

Liu, J., Curry, J. A., Wang, H., Horton, R. M., Song, M.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-07-11

Description: We respond here to three comments by Li and Wu (1) that we find to be either incorrect or lacking in relevance.As stated in Liu et al. (2), “extended from previous studies,” we demonstrated that autumn Arctic sea-ice anomalies, instead of winter North Atlantic Oscillation/Arctic Oscillation (NAO/AO) and El Niño, show a consistent relationship with winter snow anomalies for recent winters. We then demonstrated that reduction of sea ice is linked to winter atmospheric circulation change that is different from the classic winter AO and increased local moisture sources to Europe and the United States, which contributed to recent snowy...

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Publication bias and social class [Letters (Online Only)] (2012)

Francis, G.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-06-20

Description: Piff et al. (1) presented provocative evidence across seven experiments that people of a higher social class were more likely to engage in unethical behavior. A striking characteristic of the reported findings was the consistency of the results across different definitions of social class and measurements of unethical behavior. The multiple replications might appear to provide strong evidence for the claim, but the analysis here shows that they actually indicate the findings are unbelievable.All the findings in the work of Piff et al. (1) are based on statistical analyses of behavior. Support for their claim was found by rejecting a...

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Sex differences in personality and serotonin [Letters (Online Only)] (2012)

Yang, Z., Miao, D., Liu, X., Zhu, X.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-06-27

Description: In a recent article, Takahashi et al. (1) described interesting work regarding the mediating effect of honesty in the relationship between serotonin and reaction to unfairness. After reading the article with interest, we have some concerns about the study.First, only male subjects were investigated in their study (1). Sex differences in the serotonin system and personalities would potentially confound the results. Although the authors noted that sex could influence the reaction to unfairness, they ignored the sex differences in the serotonin system. Several studies have demonstrated sex differences in the serotonin system (2). Besides, sex differences in the rate of...

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Back electron transfer in DNA photolyase [Letters (Online Only)] (2012)

Brettel, K., Byrdin, M.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2012-06-06

Description: In a recent commentary, Stuchebrukhov (1) reviewed the progress in understanding DNA repair by photolyase, with special emphasis on a time-resolved study by Liu et al. (2). Among others, he raised the question of why back electron transfer (ET) to the semireduced flavin cofactor FADH° before splitting of the cyclobutane pyrimidine dimer (CPD) was slow (2.4 ns, compared with 250 ps for the preceding forward ET from the photoexcited fully reduced FADH− to the CPD), and suggested two possible reasons: the Marcus inverted region slow-down effect or the electron “is locked in a state that prevents back-transfer until the reaction...

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